The $38 billion deal would merge two of the leading players in the semiconductor industry, helping Qualcomm move beyond the smartphone market and into the Internet of Things and automotive markets. When the deal was announced, Qualcomm said that 48 percent of its revenue would come from mobile after the deal closed -- down from 61 percent before the deal.

The European Commission said that after an initial investigation, it had several specific concerns related to the Qualcomm-NXP deal. For instance, the merged company would have the ability and incentive to exclude rival suppliers from the markets for baseband chipsets and NFC/SEs chips, using bundling or tying.

Additionally, the commission said, the merger would remove semiconductor competition in the automotive market, particularly in emerging Vehicle-to-Everything ("V2X") technology. The commission also said the merged company could modify NXP's current intellectual property licensing practices, in particular in relation to NFC technology, in ways that could lead to increased royalties for customers or the exclusion of competitors.

The commission has 90 working days from now, until October 17, to finish its in-depth investigation and determine whether to green-light the deal.